LAMMPS (2 Apr 2025 - Development - d4867ab55e-modified)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
  using 1 OpenMP thread(s) per MPI task
# GJ thermostat

units   	metal
atom_style      full

boundary 	p p p
read_data argon.lmp
Reading data file ...
  orthogonal box = (0 0 0) to (32.146 32.146 32.146)
  1 by 1 by 1 MPI processor grid
  reading atoms ...
  864 atoms
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    0        0        0       
  special bond factors coul:  0        0        0       
     0 = max # of 1-2 neighbors
     0 = max # of 1-3 neighbors
     0 = max # of 1-4 neighbors
     1 = max # of special neighbors
  special bonds CPU = 0.000 seconds
  read_data CPU = 0.010 seconds
include ff-argon.lmp
#############################
#Atoms types - mass - charge#
#############################
#@ 1 atom types #!THIS LINE IS NECESSARY DON'T SPEND HOURS FINDING THAT OUT!#

variable Ar equal 1

#############
#Atom Masses#
#############

mass ${Ar}      39.903
mass 1      39.903

###########################
#Pair Potentials - Tersoff#
###########################

pair_style      lj/cubic
pair_coeff      * * 0.0102701 3.42


velocity all create 10 2357 mom yes dist gaussian
neighbor 1 bin

timestep 0.1

compute myKE all ke
compute myPE all pe

fix lang all gjf 10 10 1 26488

run 5000

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Your simulation uses code contributions which should be cited:

- GJ methods: doi:10.1080/00268976.2019.1662506

@Article{gronbech-jensen_complete_2020,
title = {Complete set of stochastic Verlet-type thermostats for correct Langevin simulations},
volume = {118},
number = {8},
url = {https://www.tandfonline.com/doi/full/10.1080/00268976.2019.1662506},
doi = {10.1080/00268976.2019.1662506},
journal = {Molecular Physics},
author = {Grønbech-Jensen, Niels},
year = {2020}
}

- GJ-I vhalf method: doi:10.1080/00268976.2019.1570369

@Article{jensen_accurate_2019,
title = {Accurate configurational and kinetic statistics in discrete-time Langevin systems},
volume = {117},
url = {https://www.tandfonline.com/doi/full/10.1080/00268976.2019.1570369},
doi = {10.1080/00268976.2019.1570369},
number = {18},
journal = {Molecular Physics},
author = {Jensen, Lucas Frese Grønbech and Grønbech-Jensen, Niels},
year = {2019}
}

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 6.9407173
  ghost atom cutoff = 6.9407173
  binsize = 3.4703587, bins = 10 10 10
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/cubic, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 6.481 | 6.481 | 6.481 Mbytes
   Step          Temp          E_pair         E_mol          TotEng         Press     
         0   10            -56.207652      0             -55.092137      33.341103    
      5000   9.7731898     -55.150518      0             -54.060304      322.94195    
Loop time of 2.28421 on 1 procs for 5000 steps with 864 atoms

Performance: 18912.438 ns/day, 0.001 hours/ns, 2188.940 timesteps/s, 1.891 Matom-step/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 1.2715     | 1.2715     | 1.2715     |   0.0 | 55.66
Bond    | 0.00057126 | 0.00057126 | 0.00057126 |   0.0 |  0.03
Neigh   | 0.27008    | 0.27008    | 0.27008    |   0.0 | 11.82
Comm    | 0.057938   | 0.057938   | 0.057938   |   0.0 |  2.54
Output  | 6.1954e-05 | 6.1954e-05 | 6.1954e-05 |   0.0 |  0.00
Modify  | 0.658      | 0.658      | 0.658      |   0.0 | 28.81
Other   |            | 0.0261     |            |       |  1.14

Nlocal:            864 ave         864 max         864 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:           1593 ave        1593 max        1593 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:          18143 ave       18143 max       18143 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 18143
Ave neighs/atom = 20.998843
Ave special neighs/atom = 0
Neighbor list builds = 258
Dangerous builds = 0

fix energies all ave/time 1 20000 20000 c_myKE c_myPE #file ave.out

thermo 2000
run 35000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 6.481 | 6.481 | 6.481 Mbytes
   Step          Temp          E_pair         E_mol          TotEng         Press     
      5000   9.7731898     -55.150518      0             -54.060304      322.94195    
      6000   10.024842     -55.108242      0             -53.989956      336.6125     
      8000   10.118994     -55.092171      0             -53.963382      340.42078    
     10000   10.541359     -55.100316      0             -53.924412      340.09986    
     12000   10.023234     -55.07343       0             -53.955323      345.70551    
     14000   9.5912018     -55.115121      0             -54.045208      333.43739    
     16000   9.9450498     -55.077813      0             -53.968428      343.49906    
     18000   10.113744     -55.12201       0             -53.993806      332.32214    
     20000   9.9345204     -55.176339      0             -54.068128      316.83219    
     22000   10.585719     -55.110505      0             -53.929652      336.86599    
     24000   10.024757     -55.120592      0             -54.002315      333.13056    
     26000   9.7787474     -55.116664      0             -54.02583       332.51437    
     28000   9.6092087     -55.130413      0             -54.058491      328.69165    
     30000   9.8245787     -55.057678      0             -53.961731      350.86255    
     32000   10.066994     -55.08989       0             -53.966902      341.49724    
     34000   9.5677059     -55.17222       0             -54.104928      316.06902    
     36000   9.7252627     -55.079475      0             -53.994608      343.13769    
     38000   10.438984     -55.108991      0             -53.944506      336.32562    
     40000   10.238268     -55.080817      0             -53.938723      345.13228    
Loop time of 19.138 on 1 procs for 35000 steps with 864 atoms

Performance: 15801.041 ns/day, 0.002 hours/ns, 1828.824 timesteps/s, 1.580 Matom-step/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 11.568     | 11.568     | 11.568     |   0.0 | 60.44
Bond    | 0.0042372  | 0.0042372  | 0.0042372  |   0.0 |  0.02
Neigh   | 2.2577     | 2.2577     | 2.2577     |   0.0 | 11.80
Comm    | 0.42841    | 0.42841    | 0.42841    |   0.0 |  2.24
Output  | 0.00060128 | 0.00060128 | 0.00060128 |   0.0 |  0.00
Modify  | 4.694      | 4.694      | 4.694      |   0.0 | 24.53
Other   |            | 0.1852     |            |       |  0.97

Nlocal:            864 ave         864 max         864 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:           1592 ave        1592 max        1592 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:          18144 ave       18144 max       18144 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 18144
Ave neighs/atom = 21
Ave special neighs/atom = 0
Neighbor list builds = 2122
Dangerous builds = 0
Total wall time: 0:00:21
